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Quantitative proteomics: aptamer-based quantitation of proteins

5 minute read

Published:

The aptamer-based SomaScan® assay is one of the popular methods of measuring abundances of protein targets. There is very little information on correlation between mass spectrometry (MS)-based proteomics, SOMAscan and Olink assays; Olink is another popular high throughput antibody-based platform. Some studies also reported a measurement variation between those platforms. In general aptamers/SOMAmers are selected against target proteins in their native conformation and in some cases against a functional protein with “known” post translational modifications (PTMs). It’s well known that novel PTMs (pathogen or disease-induced) can impact the protein structure, electrophilicity and interactions with proteins. The other main disadvantage is quantification which is based on DNA microarray chips (background noise). The main advantages are lower cost and data analysis.

Kaplan-Meier Curve using R

2 minute read

Published:

Kaplan-Meier curve shows what the probability of an event (for example, survival) at a certain time interval. The log-rank test compares the survival curves of two or more groups. With a small subset of patients, the Kaplan-Meier estimates can be misleading and should be interpreted with caution.

Annotation of genetic variants

4 minute read

Published:

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.

ATAC-seq peak calling with MACS2

2 minute read

Published:

ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification.

Taxonomic and functional profiling of the microbiome - whole genome shotgun metagenomics

1 minute read

Published:

This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions.

eQTL analysis of RNA-Seq data

1 minute read

Published:

Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels.
Based on the hg38 reference genome, paired-end reads are mapped by STAR aligner. The mapped reads are used for expression quantification without assembling transcripts by counting the number of reads that map to an exon by HTSeq that uses Refseq gene annotations. Then, to correct for systematic variability such as library fragment size, sequence composition bias, and read depth the raw counts are normalized as trimmed mean of M-values (TMM) through edgeR.

Quality control for GWAS studies

1 minute read

Published:

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings.

Copy number variation discovery workflows using NGS data.

less than 1 minute read

Published:

Copy number variations (CNVs) represent gain or loss of genomic regions. CNVs transmit from parents to offspring or arise de novo and play important role in neuro-psychiatric disorders and cancers.

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publications

Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC).

Published in PLOS ONE, 2020

Cancer Genomics

Recommended citation: Nabil F. Saba NF*, Dinasarapu AR*, Magliocca KR, Dwivedi B, Seby S, Qin ZS, Patel M, Griffith CC, Wang X, El-Deiry M, Steuer CE, Kowalski J, Shin DM, Zwick ME, Chen ZG (2020). "Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC)." PLOS ONE 15(9): e0238497. https://doi.org/10.1371/journal.pone.0238497

Differential expression of striatal proteins in a mouse model of DOPA-responsive dystonia reveals shared mechanisms among dystonic disorders.

Published in Molecular Genetics and Metabolism, 2021

Neuroscience

Recommended citation: Briscione MA, Dinasarapu AR, Bagchi P, Donsante Y, Downs AM, Fan X, Hoehner J, Jinnah HA, Hess EJ (2021). "Differential expression of striatal proteins in a mouse model of DOPA-responsive dystonia reveals shared mechanisms among dystonic disorders." Molecular Genetics and Metabolism. 133(4):352-361. https://doi.org/10.1016/j.ymgme.2021.05.010

Combinatorial clinically driven blood biomarker functional genomics significantly enhances genotype-phenotype resolution and diagnostics in neuromuscular disease.

Published in medRxiv, 2021

Functional Genomics

Recommended citation: Chakravorty S, Berger L, Rufibach L, Gloster L, Emmons A, Shenoy S, Hegde M, Dinasarapu AR, Gibson G (2021) Combinatorial clinically driven blood biomarker functional genomics significantly enhances genotype-phenotype resolution and diagnostics in neuromuscular disease." medRxiv https://doi.org/10.1101/2021.01.14.21249850

Circulating integrin α4β7+ CD4 T cells are enriched for proliferative transcriptional programs in HIV infection.

Published in FEBS Letters, 2021

Infectious diseases

Recommended citation: Lakshmanappa YS, Roh JW, Rane NN, Dinasarapu AR , Tran DD, Velu VV, Sheth AN, Ofotokun I, Amara RR, Kelley CF, Waetjen EW, Iyer SS (2021) Circulating integrin α4β7+ CD4 T cells are enriched for proliferative transcriptional programs in HIV infection" FEBS Letters. 595(17):2257-2270. https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14163

Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection.

Published in Journal of Neuroinflammation, 2022

Infectious diseases & Inflammation

Recommended citation: Hawes CE, Elizaldi SR, Beckman D, Diniz GB, Lakshmanappa YS, Ott S, Durbin-Johnson BP, Dinasarapu AR , Gompers AL, Morrison JH, Iyer SS (2022). Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection. Journal of Neuroinflammation, 19, 250. https://jneuroinflammation.biomedcentral.com/articles/10.1186/s12974-022-02610-y

Anti-inflammatory effects of recreational marijuana in virally suppressed youth with HIV-1 are reversed by use of tobacco products in combination with marijuana.

Published in Retrovirology, 2022

Infectious diseases & Inflammation

Recommended citation: Yin L, Dinasarapu AR , Borkar SA, Chang KF, De Paris K, Kim-Chang JJ, Sleasman JW, Goodenow MM (2022) Anti-inflammatory effects of recreational marijuana in virally suppressed youth with HIV-1 are reversed by use of tobacco products in combination with marijuana" Retrovirology 19, 10 (2022) https://retrovirology.biomedcentral.com/articles/10.1186/s12977-022-00594-4

Live-cell invasive phenotyping uncovers the ALK2/BMP6 iron homeostasis pathway as a therapeutic vulnerability in LKB1-mutant lung cancer.

Published in bioRxiv, 2023

Recommended citation: Koo J, Seong CS, Parker RE, Dwivedi B, Arthur RA, Dinasarapu AR, Johnston HR, Claussen H, Tucker-Burden C, Ramalingam SS, Fu H,Zhou W, Marcus AI, Gilbert-Ross M. (2023) Live-cell invasive phenotyping uncovers the ALK2/BMP6 iron homeostasis pathway as a therapeutic vulnerability in LKB1-mutant lung cancer" https://www.biorxiv.org/content/10.1101/2023.06.14.544941v1

Chronic SIV-induced neuroinflammation disrupts CCR7+CD4+ T cell immunosurveillance in the rhesus macaque brain.

Published in Journal of Clinical Investigation, 2024

Infectious diseases & Inflammation

Recommended citation: Elizaldi SR, Hawes CE, Verma A, Shaan Lakshmanappa Y, Dinasarapu AR, Schlegel BT, Rajasundaram D, Li J, Durbin-Johnson BP, Ma ZM, Pal PB, Beckman D, Ott S, Raeman R, Lifson J, Morrison JH, Iyer SS (2024). Chronic SIV-induced neuroinflammation disrupts CCR7+CD4+ T cell immunosurveillance in the rhesus macaque brain. J Clin Invest. https://pubmed.ncbi.nlm.nih.gov/38470479/

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